Research workbench
Preservation of peptide specificity during TCR-MHC contact dominated affinity enhancement of a melanoma-specific TCR
Analyse Preservation of peptide specificity during TCR-MHC contact dominated affinity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JFD
- Type
- protein
- Length
- 827 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Melanoma…
- UniProt
- P01892, P61769
- Ligands
- TAM, SO4
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 24% helix, 33% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Melanoma peptide | protein | 10 | 0% helix, 10% strand | — |
| D | High affinity TCR alpha chain | protein | 196 | 2% helix, 47% strand | — |
| E | High affinity TCR beta chain | protein | 245 | 7% helix, 51% strand | — |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.72 | 0.76 | 78 | SO4 |
| 2 | 687 | 0.70 | 0.77 | 63 | empty |
| 3 | 99 | 0.47 | 0.80 | 16 | empty |
| 4 | 98 | 0.47 | 0.81 | 19 | SO4 |
| 5 | 74 | 0.42 | 0.80 | 20 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2184 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1346 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 906 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 561 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 560 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4JFD · Preservation of peptide specificity during TCR-MHC contact dominated affinity enhancement… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 4JFD · PDBe 4JFD · UniProt P01892 · UniProt P61769
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